6ND9 Cell Adhesion Toxin date Dec 13, 2018
title Rhodocetin In Complex With The Integrin Alpha2-A Domain With
authors J.Stetefeld, M.D.Mcdougall, P.C.Loewen
compound source
Molecule: Snaclec Rhodocetin Subunit Gamma
Chain: A, D, G, J, M, P
 Organism_scientific: Calloselasma Rhodostoma
Organism_common: Malayan Pit Viper
Organism_taxid: 8717

Molecule: Snaclec Rhodocetin Subunit Delta
Chain: B, E, H, K, N, Q
Organism_scientific: Calloselasma Rhodostoma
Organism_common: Malayan Pit Viper
Organism_taxid: 8717

Molecule: Integrin Alpha-2
Chain: C, F, I, L, O, R
Synonym: Cd49 Antigen-Like Family Member B,Collagen Recepto Membrane Glycoprotein Ia,Gpia,Vla-2 Subunit Alpha;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Itga2, Cd49b
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 41
R_factor 0.229 R_Free 0.272
crystal
cell
length a length b length c angle alpha angle beta angle gamma
131.044 131.044 251.245 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand CA, CL, GOL, NA, NH4, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, J, N, P, K, E, B, H, Q, M, D, G
  • toxin activity


    • Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (443 Kb) [Save to disk]
  • Biological Unit Coordinates (6nd9.pdb1.gz) 78 Kb
  • Biological Unit Coordinates (6nd9.pdb2.gz) 78 Kb
  • Biological Unit Coordinates (6nd9.pdb3.gz) 79 Kb
  • Biological Unit Coordinates (6nd9.pdb4.gz) 78 Kb
  • Biological Unit Coordinates (6nd9.pdb5.gz) 78 Kb
  • Biological Unit Coordinates (6nd9.pdb6.gz) 78 Kb
  • LPC: Ligand-Protein Contacts for 6ND9
  • CSU: Contacts of Structural Units for 6ND9
  • Structure Factors (4347 Kb)
  • Retrieve 6ND9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6ND9 from S2C, [Save to disk]
    • View 6ND9 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 6ND9
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6nd9_J] [6nd9_D] [6nd9_R] [6nd9_B] [6nd9_G] [6nd9_F] [6nd9_O] [6nd9_P] [6nd9_A] [6nd9_L] [6nd9_E] [6nd9_Q] [6nd9_K] [6nd9_C] [6nd9_N] [6nd9_M] [6nd9_H] [6nd9_I]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6ND9
  • Community annotation for 6ND9 at PDBWiki (http://pdbwiki.org)

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